Variant report

Variant	rs12002878
Chromosome Location	chr9:103351495-103351496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103350659..103353280-chr9:103360412..103361939,2	K562	blood:
2	chr9:103348301..103352050-chr9:103353631..103357839,4	K562	blood:
3	chr9:103344131..103345927-chr9:103350360..103352204,2	MCF-7	breast:
4	chr9:103189259..103191094-chr9:103351193..103354003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12005789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1226587	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1226590	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1226591	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1236813	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1628249	0.95[ASN][1000 genomes]
rs17742370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780954	0.95[ASN][1000 genomes]
rs2780955	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2780956	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2780960	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2800280	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2800281	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2800283	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2800285	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2800289	0.95[ASN][1000 genomes]
rs2800290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs57290629	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60422299	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951868	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
2	chr9:103329800-103351800	Weak transcription	Ovary	ovary
3	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:103330400-103351600	Weak transcription	Fetal Stomach	stomach
5	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:103332400-103351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
8	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
9	chr9:103337600-103352200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:103338800-103352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:103340600-103351800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:103343200-103360600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:103344200-103352200	Weak transcription	Brain Angular Gyrus	brain
14	chr9:103345800-103351800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:103346200-103359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:103346600-103353600	Weak transcription	Psoas Muscle	Psoas
17	chr9:103348400-103351800	Weak transcription	Brain Substantia Nigra	brain
18	chr9:103348400-103353400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:103348600-103361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:103348800-103360600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:103349000-103353200	Enhancers	HUVEC	blood vessel
22	chr9:103349200-103352200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:103349200-103353000	Weak transcription	Brain Anterior Caudate	brain
24	chr9:103349600-103360800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:103349800-103352000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:103349800-103359400	Weak transcription	Brain Germinal Matrix	brain
27	chr9:103350000-103352000	Weak transcription	HSMM	muscle
28	chr9:103350000-103352000	Weak transcription	NHEK	skin
29	chr9:103350000-103352200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:103350000-103352400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:103350000-103352400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:103350000-103352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:103350000-103353200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:103350000-103353600	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:103350000-103357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:103350000-103357600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:103350000-103360200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:103350200-103351600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:103350200-103351600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:103350200-103352200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:103350200-103357600	Weak transcription	Fetal Brain Female	brain
42	chr9:103350200-103360200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:103350400-103357600	Weak transcription	Hela-S3	cervix
44	chr9:103350400-103359200	Weak transcription	Fetal Heart	heart
45	chr9:103350400-103360000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:103350600-103352000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:103350600-103360800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:103350800-103357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:103351000-103351800	Genic enhancers	HSMMtube	muscle
50	chr9:103351000-103352000	Weak transcription	A549	lung

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